Calcium in PDB 7mg7: Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac, PDB code: 7mg7 was solved by B.E.Partridge, P.H.Winegar, C.A.Mirkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.62 / 1.75
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.869, 70.4, 125.09, 90, 90, 90
R / Rfree (%)	18.6 / 21.5

The structure of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac (pdb code 7mg7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac, PDB code: 7mg7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:21.9 occ:1.00 O A:TYR12 2.3 21.3 1.0 OD2 A:ASP19 2.3 25.4 1.0 O A:HOH490 2.4 21.9 1.0 OD1 A:ASP10 2.4 21.2 1.0 OD1 A:ASN14 2.4 25.3 1.0 O A:HOH416 2.4 20.2 1.0 OD2 A:ASP10 2.4 19.2 1.0 CG A:ASP10 2.7 19.1 1.0 CG A:ASP19 3.4 25.2 1.0 CG A:ASN14 3.5 26.0 1.0 C A:TYR12 3.5 22.1 1.0 OD1 A:ASP19 3.8 23.9 1.0 N A:ASN14 4.0 24.4 1.0 CB A:ASN14 4.1 26.7 1.0 MN A:MN301 4.1 25.0 1.0 CB A:ASP10 4.2 18.9 1.0 CA A:TYR12 4.4 23.4 1.0 O A:HOH462 4.5 23.2 1.0 N A:PRO13 4.5 26.4 1.0 N A:TYR12 4.5 21.6 1.0 CA A:PRO13 4.5 28.6 1.0 CE1 A:HIS24 4.5 22.1 1.0 O A:ASP208 4.6 19.1 1.0 C A:PRO13 4.6 26.4 1.0 CB A:TYR12 4.6 21.6 1.0 ND2 A:ASN14 4.6 23.4 1.0 OD1 A:ASP208 4.6 21.3 1.0 CB A:ASP19 4.7 24.4 1.0 CB A:ARG228 4.7 23.5 1.0 CA A:ASN14 4.7 24.6 1.0 CA A:ARG228 4.7 21.7 1.0 O A:ARG228 4.8 21.7 1.0 NE2 A:HIS24 4.8 22.5 1.0 CD1 A:TYR12 4.9 23.4 1.0

Calcium binding site 2 out of 2 in the Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Concanavalin A Bound to A Dna Glycoconjugate, Man-Gtac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:23.4 occ:1.00 O B:TYR12 2.3 24.6 1.0 O B:HOH500 2.3 23.0 1.0 O B:HOH452 2.3 23.4 1.0 OD2 B:ASP19 2.4 26.9 1.0 OD1 B:ASP10 2.4 21.7 1.0 OD1 B:ASN14 2.4 24.4 1.0 OD2 B:ASP10 2.5 20.9 1.0 CG B:ASP10 2.7 17.4 1.0 CG B:ASP19 3.5 28.2 1.0 C B:TYR12 3.5 23.3 1.0 CG B:ASN14 3.5 28.3 1.0 OD1 B:ASP19 3.9 22.6 1.0 N B:ASN14 4.0 25.9 1.0 CB B:ASN14 4.1 29.6 1.0 MN B:MN301 4.2 27.3 1.0 CB B:ASP10 4.3 20.1 1.0 CA B:TYR12 4.3 25.8 1.0 N B:TYR12 4.4 22.9 1.0 N B:PRO13 4.5 27.5 1.0 O B:HOH425 4.5 25.8 1.0 CB B:TYR12 4.5 23.0 1.0 CA B:PRO13 4.5 27.8 1.0 O B:ASP208 4.6 23.6 1.0 C B:PRO13 4.6 26.3 1.0 CE1 B:HIS24 4.6 23.3 1.0 ND2 B:ASN14 4.6 25.4 1.0 OD1 B:ASP208 4.7 23.1 1.0 CB B:ASP19 4.7 27.0 1.0 CA B:ASN14 4.7 28.5 1.0 CB B:ARG228 4.7 26.1 1.0 CA B:ARG228 4.8 23.6 1.0 CD2 B:TYR12 4.9 25.2 1.0 O B:ARG228 4.9 25.5 1.0 NE2 B:HIS24 4.9 26.5 1.0 CD1 B:ILE17 5.0 49.5 1.0

B.E.Partridge, P.H.Winegar, Z.Han, C.A.Mirkin. Redefining Protein Interfaces Within Protein Single Crystals with Dna Journal of the American 2021CHEMICAL Society.
DOI: 10.1021/JACS.1C04191